Date: Sun, 4 Jul 2021 00:17:13 GMT From: pkg-fallout@FreeBSD.org To: yuri@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - 114amd64-default][biology/abyss] Failed for abyss-2.3.1 in build Message-ID: <202107040017.1640HDE9016119@beefy9.nyi.freebsd.org>
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You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: yuri@FreeBSD.org Log URL: http://beefy9.nyi.freebsd.org/data/114amd64-default/6e40bf8661e0/logs/abyss-2.3.1.log Build URL: http://beefy9.nyi.freebsd.org/build.html?mastername=114amd64-default&build=6e40bf8661e0 Log: =>> Building biology/abyss build started at Sun Jul 4 00:09:32 UTC 2021 port directory: /usr/ports/biology/abyss package name: abyss-2.3.1 building for: FreeBSD 114amd64-default-job-02 11.4-RELEASE-p12 FreeBSD 11.4-RELEASE-p12 amd64 maintained by: yuri@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-8-gaf08dbda Host OSVERSION: 1400008 Jail OSVERSION: 1104001 Job Id: 02 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1104001 UNAME_v=FreeBSD 11.4-RELEASE-p12 UNAME_r=11.4-RELEASE-p12 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 HOME=/root PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin LOCALBASE=/usr/local USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-8-gaf08dbda MASTERMNT=/usr/local/poudriere/data/.m/114amd64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/114amd64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=114amd64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/114amd64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ===> The following configuration options are available for abyss-2.3.1: DOCS=on: Build and/or install documentation ===> Use 'make config' to modify these settings ---End OPTIONS List--- --MAINTAINER-- yuri@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --without-sparsehash --prefix=/usr/local ${_LATE_CONFIGURE_ARGS} --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- MAKE=gmake XDG_DATA_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/abyss/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CMAKE_PREFIX_PATH="/usr/local" CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288 --End CONFIGURE_ENV-- --MAKE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/biology/abyss/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/abyss/work HOME=/wrkdirs/usr/ports/biology/abyss/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/abyss/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing " CPP="cpp" CPPFLAGS="-isystem /usr/local/include" LDFLAGS=" -fstack-protector-strong -L/usr/local/lib " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include " MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install -s -m 555" BSD_INSTALL_LIB="install -s -m 0644" BSD_INSTALL_SCRIPT="install -m 555" BSD_INSTALL_DATA="install -m 0644" BSD_INSTALL_MAN="install -m 444" --End MAKE_ENV-- --PLIST_SUB-- PORTDOCS="" OSREL=11.4 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/abyss" EXAMPLESDIR="share/examples/abyss" DATADIR="share/abyss" WWWDIR="www/abyss" ETCDIR="etc/abyss" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/abyss DOCSDIR=/usr/local/share/doc/abyss EXAMPLESDIR=/usr/local/share/examples/abyss WWWDIR=/usr/local/www/abyss ETCDIR=/usr/local/etc/abyss --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /usr/local/etc/poudriere.d/make.conf #### # XXX: We really need this but cannot use it while 'make checksum' does not # try the next mirror on checksum failure. It currently retries the same # failed mirror and then fails rather then trying another. It *does* # try the next if the size is mismatched though. #MASTER_SITE_FREEBSD=yes # Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs MAKE_JOBS_NUMBER=2 #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: x86_64-unknown-freebsd11.4 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: x86_64-unknown-freebsd11.4 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o" CC_OUTPUT_921dbbb2_58173849=yes CC_OUTPUT_921dbbb2_9bdba57c=yes CC_OUTPUT_921dbbb2_6a4fe7f5=yes CC_OUTPUT_921dbbb2_6bcac02b=yes CC_OUTPUT_921dbbb2_67d20829=yes CC_OUTPUT_921dbbb2_bfa62e83=yes CC_OUTPUT_921dbbb2_f0b4d593=yes CC_OUTPUT_921dbbb2_308abb44=yes CC_OUTPUT_921dbbb2_f00456e5=yes CC_OUTPUT_921dbbb2_65ad290d=yes CC_OUTPUT_921dbbb2_f2776b26=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: x86_64-unknown-freebsd11.4 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=amd64 OPSYS=FreeBSD _OSRELEASE=11.4-RELEASE-p12 OSREL=11.4 OSVERSION=1104001 PYTHONBASE=/usr/local HAVE_COMPAT_IA32_KERN=YES CONFIGURE_MAX_CMD_LEN=524288 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=0 DISABLE_MAKE_JOBS=poudriere ---End make.conf--- --Resource limits-- cpu time (seconds, -t) unlimited file size (512-blocks, -f) unlimited data seg size (kbytes, -d) 33554432 stack size (kbytes, -s) 524288 core file size (512-blocks, -c) unlimited max memory size (kbytes, -m) unlimited locked memory (kbytes, -l) unlimited max user processes (-u) 89999 open files (-n) 1024 virtual mem size (kbytes, -v) unlimited swap limit (kbytes, -w) unlimited socket buffer size (bytes, -b) unlimited pseudo-terminals (-p) unlimited kqueues (-k) unlimited umtx shared locks (-o) unlimited --End resource limits-- =======================<phase: check-sanity >============================ ===> License GPLv3 accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> abyss-2.3.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.16.3.txz [114amd64-default-job-02] Installing pkg-1.16.3... [114amd64-default-job-02] Extracting pkg-1.16.3: .......... done ===> abyss-2.3.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of abyss-2.3.1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by abyss-2.3.1 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by abyss-2.3.1 for building => SHA256 Checksum OK for bcgsc-abyss-2.3.1_GH0.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by abyss-2.3.1 for building ===> Extracting for abyss-2.3.1 => SHA256 Checksum OK for bcgsc-abyss-2.3.1_GH0.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for abyss-2.3.1 ===> Applying FreeBSD patches for abyss-2.3.1 from /usr/ports/biology/abyss/files =========================================================================== =======================<phase: build-depends >============================ ===> abyss-2.3.1 depends on file: /usr/local/include/boost/version.hpp - not found ===> Installing existing package /packages/All/boost-libs-1.72.0_5.txz [114amd64-default-job-02] Installing boost-libs-1.72.0_5... [114amd64-default-job-02] `-- Installing icu-69.1,1... [114amd64-default-job-02] `-- Extracting icu-69.1,1: .......... done [114amd64-default-job-02] Extracting boost-libs-1.72.0_5: .......... done ===== Message from boost-libs-1.72.0_5: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===> abyss-2.3.1 depends on file: /usr/local/include/boost/version.hpp - found ===> Returning to build of abyss-2.3.1 <snip> mv -f .deps/konnector-konnector.Tpo .deps/konnector-konnector.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o konnector konnector-konnector.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Konnector' Making all in Consensus gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Consensus' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Consensus-Consensus.o -MD -MP -MF .deps/Consensus-Consensus.Tpo -c -o Consensus-Consensus.o `test -f 'Consensus.cpp' || echo './'`Consensus.cpp mv -f .deps/Consensus-Consensus.Tpo .deps/Consensus-Consensus.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o Consensus Consensus-Consensus.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Consensus' Making all in DAssembler gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/DAssembler' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DAssembler-DAssembler.o -MD -MP -MF .deps/DAssembler-DAssembler.Tpo -c -o DAssembler-DAssembler.o `test -f 'DAssembler.cpp' || echo './'`DAssembler.cpp mv -f .deps/DAssembler-DAssembler.Tpo .deps/DAssembler-DAssembler.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DAssembler-RotatedRead.o -MD -MP -MF .deps/DAssembler-RotatedRead.Tpo -c -o DAssembler-RotatedRead.o `test -f 'RotatedRead.cpp' || echo './'`RotatedRead.cpp mv -f .deps/DAssembler-RotatedRead.Tpo .deps/DAssembler-RotatedRead.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o DAssembler DAssembler-DAssembler.o DAssembler-RotatedRead.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/DAssembler' Making all in DistanceEst gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/DistanceEst' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst-DistanceEst.o -MD -MP -MF .deps/DistanceEst-DistanceEst.Tpo -c -o DistanceEst-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp mv -f .deps/DistanceEst-DistanceEst.Tpo .deps/DistanceEst-DistanceEst.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst-MLE.o -MD -MP -MF .deps/DistanceEst-MLE.Tpo -c -o DistanceEst-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp mv -f .deps/DistanceEst-MLE.Tpo .deps/DistanceEst-MLE.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o DistanceEst DistanceEst-DistanceEst.o DistanceEst-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst_ssq-DistanceEst.o -MD -MP -MF .deps/DistanceEst_ssq-DistanceEst.Tpo -c -o DistanceEst_ssq-DistanceEst.o `test -f 'DistanceEst.cpp' || echo './'`DistanceEst.cpp mv -f .deps/DistanceEst_ssq-DistanceEst.Tpo .deps/DistanceEst_ssq-DistanceEst.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT DistanceEst_ssq-MLE.o -MD -MP -MF .deps/DistanceEst_ssq-MLE.Tpo -c -o DistanceEst_ssq-MLE.o `test -f 'MLE.cpp' || echo './'`MLE.cpp mv -f .deps/DistanceEst_ssq-MLE.Tpo .deps/DistanceEst_ssq-MLE.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o DistanceEst-ssq DistanceEst_ssq-DistanceEst.o DistanceEst_ssq-MLE.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/DistanceEst' Making all in KAligner gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/KAligner' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT KAligner-KAligner.o -MD -MP -MF .deps/KAligner-KAligner.Tpo -c -o KAligner-KAligner.o `test -f 'KAligner.cpp' || echo './'`KAligner.cpp mv -f .deps/KAligner-KAligner.Tpo .deps/KAligner-KAligner.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT KAligner-Aligner.o -MD -MP -MF .deps/KAligner-Aligner.Tpo -c -o KAligner-Aligner.o `test -f 'Aligner.cpp' || echo './'`Aligner.cpp mv -f .deps/KAligner-Aligner.Tpo .deps/KAligner-Aligner.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o KAligner KAligner-KAligner.o KAligner-Aligner.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -lpthread -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/KAligner' Making all in Layout gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Layout' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_layout-layout.o -MD -MP -MF .deps/abyss_layout-layout.Tpo -c -o abyss_layout-layout.o `test -f 'layout.cc' || echo './'`layout.cc mv -f .deps/abyss_layout-layout.Tpo .deps/abyss_layout-layout.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-layout abyss_layout-layout.o ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Layout' Making all in LogKmerCount gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/LogKmerCount' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT logcounter-logcounter.o -MD -MP -MF .deps/logcounter-logcounter.Tpo -c -o logcounter-logcounter.o `test -f 'logcounter.cc' || echo './'`logcounter.cc mv -f .deps/logcounter-logcounter.Tpo .deps/logcounter-logcounter.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o logcounter logcounter-logcounter.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/LogKmerCount' Making all in Map gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Map' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_index-index.o -MD -MP -MF .deps/abyss_index-index.Tpo -c -o abyss_index-index.o `test -f 'index.cc' || echo './'`index.cc mv -f .deps/abyss_index-index.Tpo .deps/abyss_index-index.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-index abyss_index-index.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_map-map.o -MD -MP -MF .deps/abyss_map-map.Tpo -c -o abyss_map-map.o `test -f 'map.cc' || echo './'`map.cc mv -f .deps/abyss_map-map.Tpo .deps/abyss_map-map.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-map abyss_map-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_map_ssq-map.o -MD -MP -MF .deps/abyss_map_ssq-map.Tpo -c -o abyss_map_ssq-map.o `test -f 'map.cc' || echo './'`map.cc mv -f .deps/abyss_map_ssq-map.Tpo .deps/abyss_map_ssq-map.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-map-ssq abyss_map_ssq-map.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../FMIndex -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_overlap-overlap.o -MD -MP -MF .deps/abyss_overlap-overlap.Tpo -c -o abyss_overlap-overlap.o `test -f 'overlap.cc' || echo './'`overlap.cc mv -f .deps/abyss_overlap-overlap.Tpo .deps/abyss_overlap-overlap.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-overlap abyss_overlap-overlap.o ../FMIndex/libfmindex.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Map' Making all in MergePaths gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/MergePaths' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT MergePaths-MergePaths.o -MD -MP -MF .deps/MergePaths-MergePaths.Tpo -c -o MergePaths-MergePaths.o `test -f 'MergePaths.cpp' || echo './'`MergePaths.cpp mv -f .deps/MergePaths-MergePaths.Tpo .deps/MergePaths-MergePaths.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o MergePaths MergePaths-MergePaths.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT MergeContigs-MergeContigs.o -MD -MP -MF .deps/MergeContigs-MergeContigs.Tpo -c -o MergeContigs-MergeContigs.o `test -f 'MergeContigs.cpp' || echo './'`MergeContigs.cpp mv -f .deps/MergeContigs-MergeContigs.Tpo .deps/MergeContigs-MergeContigs.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o MergeContigs MergeContigs-MergeContigs.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I../SimpleGraph -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT PathConsensus-PathConsensus.o -MD -MP -MF .deps/PathConsensus-PathConsensus.Tpo -c -o PathConsensus-PathConsensus.o `test -f 'PathConsensus.cpp' || echo './'`PathConsensus.cpp mv -f .deps/PathConsensus-PathConsensus.Tpo .deps/PathConsensus-PathConsensus.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o PathConsensus PathConsensus-PathConsensus.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/MergePaths' Making all in Overlap gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Overlap' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT Overlap-Overlap.o -MD -MP -MF .deps/Overlap-Overlap.Tpo -c -o Overlap-Overlap.o `test -f 'Overlap.cpp' || echo './'`Overlap.cpp mv -f .deps/Overlap-Overlap.Tpo .deps/Overlap-Overlap.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o Overlap Overlap-Overlap.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Overlap' Making all in PairedDBG gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PairedDBG' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_paired_dbg-abyss-paired-dbg.o -MD -MP -MF .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo -c -o abyss_paired_dbg-abyss-paired-dbg.o `test -f 'abyss-paired-dbg.cc' || echo './'`abyss-paired-dbg.cc mv -f .deps/abyss_paired_dbg-abyss-paired-dbg.Tpo .deps/abyss_paired_dbg-abyss-paired-dbg.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -DPAIRED_DBG -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_paired_dbg-KmerPair.o -MD -MP -MF .deps/abyss_paired_dbg-KmerPair.Tpo -c -o abyss_paired_dbg-KmerPair.o `test -f 'KmerPair.cc' || echo './'`KmerPair.cc mv -f .deps/abyss_paired_dbg-KmerPair.Tpo .deps/abyss_paired_dbg-KmerPair.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-paired-dbg abyss_paired_dbg-abyss-paired-dbg.o abyss_paired_dbg-KmerPair.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a ../DataBase/libdb.a -lsqlite3 -ldl -lm -ldl -lm depbase=`echo KmerPair.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\ c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT KmerPair.o -MD -MP -MF $depbase.Tpo -c -o KmerPair.o KmerPair.cc &&\ mv -f $depbase.Tpo $depbase.Po rm -f libpaireddbg.a ar cru libpaireddbg.a KmerPair.o ranlib libpaireddbg.a gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PairedDBG' Making all in ParseAligns gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/ParseAligns' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_fixmate-abyss-fixmate.o -MD -MP -MF .deps/abyss_fixmate-abyss-fixmate.Tpo -c -o abyss_fixmate-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc mv -f .deps/abyss_fixmate-abyss-fixmate.Tpo .deps/abyss_fixmate-abyss-fixmate.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-fixmate abyss_fixmate-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_fixmate_ssq-abyss-fixmate.o -MD -MP -MF .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo -c -o abyss_fixmate_ssq-abyss-fixmate.o `test -f 'abyss-fixmate.cc' || echo './'`abyss-fixmate.cc mv -f .deps/abyss_fixmate_ssq-abyss-fixmate.Tpo .deps/abyss_fixmate_ssq-abyss-fixmate.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-fixmate-ssq abyss_fixmate_ssq-abyss-fixmate.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT ParseAligns-ParseAligns.o -MD -MP -MF .deps/ParseAligns-ParseAligns.Tpo -c -o ParseAligns-ParseAligns.o `test -f 'ParseAligns.cpp' || echo './'`ParseAligns.cpp mv -f .deps/ParseAligns-ParseAligns.Tpo .deps/ParseAligns-ParseAligns.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o ParseAligns ParseAligns-ParseAligns.o ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/ParseAligns' Making all in PathOverlap gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PathOverlap' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT PathOverlap-PathOverlap.o -MD -MP -MF .deps/PathOverlap-PathOverlap.Tpo -c -o PathOverlap-PathOverlap.o `test -f 'PathOverlap.cpp' || echo './'`PathOverlap.cpp mv -f .deps/PathOverlap-PathOverlap.Tpo .deps/PathOverlap-PathOverlap.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o PathOverlap PathOverlap-PathOverlap.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PathOverlap' Making all in PopBubbles gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PopBubbles' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Align -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT PopBubbles-PopBubbles.o -MD -MP -MF .deps/PopBubbles-PopBubbles.Tpo -c -o PopBubbles-PopBubbles.o `test -f 'PopBubbles.cpp' || echo './'`PopBubbles.cpp mv -f .deps/PopBubbles-PopBubbles.Tpo .deps/PopBubbles-PopBubbles.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o PopBubbles PopBubbles-PopBubbles.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a ../dialign/libdialign.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/PopBubbles' Making all in Scaffold gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Scaffold' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_scaffold-scaffold.o -MD -MP -MF .deps/abyss_scaffold-scaffold.Tpo -c -o abyss_scaffold-scaffold.o `test -f 'scaffold.cc' || echo './'`scaffold.cc mv -f .deps/abyss_scaffold-scaffold.Tpo .deps/abyss_scaffold-scaffold.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-scaffold abyss_scaffold-scaffold.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_junction-junction.o -MD -MP -MF .deps/abyss_junction-junction.Tpo -c -o abyss_junction-junction.o `test -f 'junction.cc' || echo './'`junction.cc mv -f .deps/abyss_junction-junction.Tpo .deps/abyss_junction-junction.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-junction abyss_junction-junction.o ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_longseqdist-longseqdist.o -MD -MP -MF .deps/abyss_longseqdist-longseqdist.Tpo -c -o abyss_longseqdist-longseqdist.o `test -f 'longseqdist.cpp' || echo './'`longseqdist.cpp mv -f .deps/abyss_longseqdist-longseqdist.Tpo .deps/abyss_longseqdist-longseqdist.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-longseqdist abyss_longseqdist-longseqdist.o ../Common/libcommon.a -ldl -lm c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_drawgraph-drawgraph.o -MD -MP -MF .deps/abyss_drawgraph-drawgraph.Tpo -c -o abyss_drawgraph-drawgraph.o `test -f 'drawgraph.cc' || echo './'`drawgraph.cc mv -f .deps/abyss_drawgraph-drawgraph.Tpo .deps/abyss_drawgraph-drawgraph.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-drawgraph abyss_drawgraph-drawgraph.o ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Scaffold' Making all in SimpleGraph gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/SimpleGraph' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -Wno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT SimpleGraph-SimpleGraph.o -MD -MP -MF .deps/SimpleGraph-SimpleGraph.Tpo -c -o SimpleGraph-SimpleGraph.o `test -f 'SimpleGraph.cpp' || echo './'`SimpleGraph.cpp mv -f .deps/SimpleGraph-SimpleGraph.Tpo .deps/SimpleGraph-SimpleGraph.Po c++ -std=c++11 -Wall -Wextra -Werror -Wno-strict-aliasing -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o SimpleGraph SimpleGraph-SimpleGraph.o ../DataBase/libdb.a -lsqlite3 -ldl -lm ../Common/libcommon.a -lpthread -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/SimpleGraph' Making all in kmerprint gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/kmerprint' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Assembly -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT kmerprint-kmerprint.o -MD -MP -MF .deps/kmerprint-kmerprint.Tpo -c -o kmerprint-kmerprint.o `test -f 'kmerprint.cc' || echo './'`kmerprint.cc mv -f .deps/kmerprint-kmerprint.Tpo .deps/kmerprint-kmerprint.Po c++ -std=c++11 -Wall -Wextra -Werror -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o kmerprint kmerprint-kmerprint.o ../Assembly/libassembly.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/kmerprint' Making all in FilterGraph gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/FilterGraph' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_filtergraph-FilterGraph.o -MD -MP -MF .deps/abyss_filtergraph-FilterGraph.Tpo -c -o abyss_filtergraph-FilterGraph.o `test -f 'FilterGraph.cc' || echo './'`FilterGraph.cc mv -f .deps/abyss_filtergraph-FilterGraph.Tpo .deps/abyss_filtergraph-FilterGraph.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-filtergraph abyss_filtergraph-FilterGraph.o ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/FilterGraph' Making all in GapFiller gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/GapFiller' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I../Align -D SAM_SEQ_QUAL=1 -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_gapfill-gapfill.o -MD -MP -MF .deps/abyss_gapfill-gapfill.Tpo -c -o abyss_gapfill-gapfill.o `test -f 'gapfill.cpp' || echo './'`gapfill.cpp mv -f .deps/abyss_gapfill-gapfill.Tpo .deps/abyss_gapfill-gapfill.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-gapfill abyss_gapfill-gapfill.o ../Align/libalign.a ../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/GapFiller' Making all in Sealer gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Sealer' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_sealer-sealer.o -MD -MP -MF .deps/abyss_sealer-sealer.Tpo -c -o abyss_sealer-sealer.o `test -f 'sealer.cc' || echo './'`sealer.cc mv -f .deps/abyss_sealer-sealer.Tpo .deps/abyss_sealer-sealer.Po c++ -std=c++11 -Wall -Wextra -Werror -fopenmp -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -fstack-protector-strong -L/usr/local/lib -o abyss-sealer abyss_sealer-sealer.o ../DataLayer/libdatalayer.a ../Align/libalign.a ../Common/libcommon.a -ldl -lm pandoc -s -o abyss-sealer.1 README.md gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/Sealer' Making all in RResolver gmake[3]: Entering directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/RResolver' c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_rresolver_short-RResolverShort.o -MD -MP -MF .deps/abyss_rresolver_short-RResolverShort.Tpo -c -o abyss_rresolver_short-RResolverShort.o `test -f 'RResolverShort.cpp' || echo './'`RResolverShort.cpp mv -f .deps/abyss_rresolver_short-RResolverShort.Tpo .deps/abyss_rresolver_short-RResolverShort.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT abyss_rresolver_short-Contigs.o -MD -MP -MF .deps/abyss_rresolver_short-Contigs.Tpo -c -o abyss_rresolver_short-Contigs.o `test -f 'Contigs.cpp' || echo './'`Contigs.cpp mv -f .deps/abyss_rresolver_short-Contigs.Tpo .deps/abyss_rresolver_short-Contigs.Po c++ -std=c++11 -DHAVE_CONFIG_H -I. -I.. -I/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1 -isystem /usr/local/include -isystem/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/boost_1_56_0 -Wall -Wextra -Werror -fopenmp -I.. -I../Common -I../DataLayer -I../RResolver/btllib/include -O2 -pipe -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -isystem /usr/local/include -MT libralgorithmsshort_a-RAlgorithmsShort.o -MD -MP -MF .deps/libralgorithmsshort_a-RAlgorithmsShort.Tpo -c -o libralgorithmsshort_a-RAlgorithmsShort.o `test -f 'RAlgorithmsShort.cpp' || echo './'`RAlgorithmsShort.cpp In file included from RAlgorithmsShort.cpp:5: ./btllib/include/btllib/seq_reader.hpp:650:14: error: use of undeclared identifier 'getline'; did you mean 'std::getline'? s.s_size = getline(&(s.s), &(s.s_cap), source); ^~~~~~~ std::getline /usr/include/c++/v1/istream:1507:1: note: 'std::getline' declared here getline(basic_istream<_CharT, _Traits>& __is, ^ In file included from RAlgorithmsShort.cpp:5: ./btllib/include/btllib/seq_reader.hpp:650:14: error: no matching function for call to 'getline' s.s_size = getline(&(s.s), &(s.s_cap), source); ^~~~~~~ /usr/include/c++/v1/istream:1507:1: note: candidate template ignored: could not match 'basic_istream<type-parameter-0-0, type-parameter-0-1>' against 'char **' getline(basic_istream<_CharT, _Traits>& __is, ^ 2 errors generated. gmake[3]: *** [Makefile:485: libralgorithmsshort_a-RAlgorithmsShort.o] Error 1 gmake[3]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1/RResolver' gmake[2]: *** [Makefile:490: all-recursive] Error 1 gmake[2]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1' gmake[1]: *** [Makefile:410: all] Error 2 gmake[1]: Leaving directory '/wrkdirs/usr/ports/biology/abyss/work/abyss-2.3.1' *** Error code 1 Stop. make: stopped in /usr/ports/biology/abyss
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